I'm a senior in college studying computer engineering, so I spend a lot of time sitting in class and/or in front of a computer. I want to commit to a fitness routine before my sedentary lifestyle starts affecting my health. Now is a good time to start since I have free access to my institution's gyms and a fairly flexible schedule.

My problem is I have no idea where to begin. Googling "workout routines" or "fitness programs" hasn't been helpful, since many of the results are geared toward rapid weight loss or "5 minute abs" garbage. I'm looking for a general fitness routine with some emphasis on hypertrophy, preferably one that is backed by research or success stories.

Currently, I'm 5'11 and ~150lbs (~68kg) so I'm a bit on the underweight side. My bench, squat, etc. aren't too impressive, nor is my cardio/endurance. I have worked out sporadically in the past, and I tried working with trainers on a couple occasions, but I never stuck with it after using up my sessions.

Find or create a concrete, easy-to-follow routine to facilitate these goals

Ideally, I want to be able to walk into the gym with a checklist of things I can knock out one by one. Motivation isn't as big of an issue when I know exactly what I've got to get done. Things to do outside of the gym are important as well.

Anyway, I hope I'm not being too vague or general here. Don't craft me a routine yourself, but rather point me to some good resources (websites, books, etc.) where I can find routines that meet my needs or at least shed some light on creating one of my own.

Both of these are by Dr. Kilgore and Mark Rippetoe. Practical programming gives you a good foundation of understanding what you need to do to customize your training program. Starting Strength has an excellent foundation on the mechanics of the lifts, along with extensive troubleshooting sections. It's also a very good program.

Based on my own journey, and the things I've learned while doing it, I would amend your goals a bit--particularly since one of them will cause some conflict with your other goals.

I recommend gaining all your beginner strength gains before aiming for hypertrophy. It takes about 3-9 months of concerted effort (depending on many variables).

For your diet, in order to gain weight, I recommend a Gallon of Milk a Day (GOMAD)--and that's whole milk. This combined with the first bullet will help you put on the weight you are looking for.

Adjust your cardio goals. Strength training (whether for aesthetics or strength) is an anaerobic activity. If you keep your running in the anaerobic range (sprints and short distance runs), you won't be undoing in your cardio what you were doing with the weight training.

The Starting Strength program is very simple, and easy to follow. You will gain a lot of strength, which will have an effect on your muscle mass and weight goals. Combine that with a month or two of GOMAD and you are right on target. Once you hit intermediate levels, you can start specializing in physique or continue with strength. I find the easy to measure and concrete goals of strength training to be more to my liking.

+1 for Starting Strength. Another site with some good reading is Stronglifts, his program is really similar to Starting Strength. If SS doesn't seem to fit you well, try the Stronglifts 5x5. Give every exercise program a chance to work, though! Don't go switching around because you don't see immediate results. Patience is one of the most important training virtues.
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parkker007Sep 2 '11 at 21:06

I started with Stronglifts and did that for 12 weeks, then switched to Starting Strength. The problem isn't the program, it's the guy promoting it. Last time I suggested someone give SL5x5 a try Medhi tried selling them a few videos that quite frankly weren't for their ability level yet. You get a better foundation of good solid knowledge with Starting Strength.
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Berin LoritschSep 3 '11 at 11:56

I have gone to a box and done the exercises with trainers, but if you know how to do the movements already (and if not, they have step by step instruction videos), you don't have to go to a box unless you like someone yelling at you to keep you motivated. The workouts change every day, which means that you will never get bored. Also, they are a big supporter of the Paleo diet.

Probably the best aspect of Crossfit for a beginner is the wide exposure to a variety of exercises. As you build experience, you'll be more and more capable of figuring out a routine on the fly that will address your needs for that day.
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Christopher BibbsSep 2 '11 at 12:28

Crossfit does give good exposure to a range of movements and activities. However, be prepared to scale all of the workouts, and be careful particularly with the high-repetition lifts. For some workouts you may want to scale weight, repetitions, or the movement to chase good form or to maintain intensity. Sometimes it is hard to do both. I'd try to perform the more exotic movements concentrating on form without worrying about intensity, whereas I'd substitute jumping pull-ups, box press-ups and the like for workouts that seem intended to keep the metabolic rate high.
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silasdavisSep 2 '11 at 15:21

I would add that your aims do seem commensurate with crossfit's. You might find you drift more towards gymnastics or Olympic lifts or some form of interval training once you gain familiarity with them through the crossfit composite
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silasdavisSep 2 '11 at 15:25

Aside from the already mentioned Crossfit, I'd recommend reading up with my personal favorite Home Workout Bible. It has good exercises and routines for a variety of goals and differing available equipment.

Cooking as a student is hard. You might want to look at something like Zonya's which focuses on healthy, quick to prepare meals. Most are scaled for four people, but you can get some down to one or two portions. She also includes useful nutrional information so you can use it to make plans about what you should be eating, not just what sounds good.